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AnalyzeCovariates

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    Lucas Kopecky Bobadilla

    I actually figure it out by running the R script alone. It seems that it is needed to transform the csv file strings to factor.

     

    By adding changing the line 16 from:

    data <- read.csv(args[1])

    to

    data <- read.csv(args[1], stringsAsFactors = TRUE)

    The R script worked. Any chance to change the script so this error stop to occur in the future?

     

    Thanks!

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    Bhanu Gandham

    Hi Lucas Kopecky Bobadilla

     

    Thank you for pointing out this issue and for helping us find a solution for it. I have created a issue ticket for this and you can follow its progress here: https://github.com/broadinstitute/gatk/issues/6650

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    Jenifer

    Hi!

    This is also happening to me. My problem is that I am working in a cluster so I cannot write at gatk directory. Do you know if I can solve this without modifying the Rscript? I am using gatk/4.1.7.0 version.

    Thanks!

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    Lucas Kopecky Bobadilla

    You may be able to contact the people responsible for the cluster to change the R script. Another solution would be to install GATK on your computer and copy the R script into the cluster and run it instead of running the GATK version from the cluster. 

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    Genevieve Brandt (she/her)

    Jenifer this should also be fixed if you can get the system administrators to update the GATK version to 4.2.0.0 since the issue ticket has been closed and fixed.

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    RAMESH GANDUSEKAR

    Hi Lucas Kopecky Bobadilla, thanks for figuring out the error.

    I stuck up at this point for a number of days trying to figure out the error. At the end, I found this page.

     

    Genevieve Brandt (she/her), I am using 4.2.0.0-1 and the error remains in the latest version too.... is it is possible for the GATK team to fix the issue. I am using a 'Cluster' and we are not supposed to make changes.

    Thanks in advance !!!

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    Genevieve Brandt (she/her)

    Hi RAMESH GANDUSEKAR,

    Thank you for updating about the current issue you are facing. Could you please post your complete command and the complete stack trace output?

    Thank you,

    Genevieve

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    Wajya Ajmal

    Hi Genevieve Brandt,

    I am using current version of GATK i.e., v4.2.2.0 and getting the same error. I used the following command: 

    gatk AnalyzeCovariates -before rice_recal_initial_data.table -after rice_recal_final_data.table -plots AnalyzeCovariates.pdf

    Error:

    [September 21, 2021 12:53:07 PM PKT] org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=619708416
    org.broadinstitute.hellbender.utils.R.RScriptExecutorException:
    Rscript exited with 127
    Command Line: Rscript -e tempLibDir = '/tmp/Rlib.468241554194418735';source('/tmp/BQSR.6414813687878758067.R'); /tmp/AnalyzeCovariates6757120775684469553.csv /home/wajya/Documents/WGS/BaseRecalibration/rice_recal_initial_data.table /home/wajya/Documents/WGS/BaseRecalibration/AnalyzeCovariates.pdf
    Stdout:
    Stderr: /home/wajya/anaconda3/envs/wgsanalysis/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

    at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:79)
    at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:18)
    at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:112)
    at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:125)
    at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:360)
    at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:329)
    at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.doWork(AnalyzeCovariates.java:341)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

    Kindly guide how to resolve this error. 

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    Genevieve Brandt (she/her)

    Thanks for following up with your command and stack trace Wajya Ajmal. This does look similar to the above error, but it is most likely caused by an issue with your R installation and not a GATK issue. This is something you'll have to look into on your end. Though definitely let me know if you have further questions.

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